X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BYRCZRB WITH ZN BOUND

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6293Protein solution 15 mg/ml protein, 20mM Tris, pH 8.0; precipitant solution 0.2M ammonium sulfate, 15% PEG 4000, 0.1M sodium acetate, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.331α = 90
b = 60.331β = 90
c = 92.137γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F1CHESSF1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.75098.90.04254.812.821179
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7692.40.3934.46.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTCZRB WITH ZN BOUND1.730.712005320053108698.90.1860.224RANDOM28.23
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.41-0.2-0.410.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.794
r_dihedral_angle_4_deg18.097
r_dihedral_angle_3_deg13.404
r_dihedral_angle_1_deg4.661
r_scangle_it4.127
r_scbond_it2.574
r_mcangle_it1.299
r_angle_refined_deg1.202
r_mcbond_it0.847
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.794
r_dihedral_angle_4_deg18.097
r_dihedral_angle_3_deg13.404
r_dihedral_angle_1_deg4.661
r_scangle_it4.127
r_scbond_it2.574
r_mcangle_it1.299
r_angle_refined_deg1.202
r_mcbond_it0.847
r_nbtor_refined0.301
r_symmetry_vdw_refined0.223
r_nbd_refined0.203
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.153
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1310
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
ARP/wARPmodel building